Uses of Package
org.biojavax.bio.seq

Packages that use org.biojavax.bio.seq

Package	Description
org.biojavax	The Biojava extensions packages, classes that extend the core biojava functionality The biojavax packages contain a number of extensions to the core biojava interfaces.
org.biojavax.bio.alignment	This package contains the interfaces that need to be implemented by discrete alignment services.
org.biojavax.bio.alignment.blast	This package holds implementations of the org.biojava3.ws.alignment interfaces for the NCBI remote QBlast services through the WWW.
org.biojavax.bio.db	Interactions between biojavax objects and a DB.
org.biojavax.bio.db.biosql	Interface between biojava and biosql databases
org.biojavax.bio.db.ncbi	Interfaces to NCBI data.
org.biojavax.bio.seq	Rich implementations of Sequences, Locations and Features.
org.biojavax.bio.seq.io	Classes to support the I/O of RichSequence and Bioentry objects.

Classes in org.biojavax.bio.seq used by org.biojavax

Class and Description
PositionResolver Resolves a position that is fuzzy or covers a range of bases by converting it to a single base.
RichLocation Describes locations, and adds the concepts of circularity, fuzziness, annotations, and cross-references to other databases.
RichSequenceHandler An interface for classes that know how to handle subsequence operations.

Classes in org.biojavax.bio.seq used by org.biojavax.bio.alignment

Class and Description
RichSequence A rich sequence is a combination of a org.biojavax.bio.Bioentry and a Sequence.

Classes in org.biojavax.bio.seq used by org.biojavax.bio.alignment.blast

Class and Description
RichSequence A rich sequence is a combination of a org.biojavax.bio.Bioentry and a Sequence.

Classes in org.biojavax.bio.seq used by org.biojavax.bio.db

Class and Description
RichSequence A rich sequence is a combination of a org.biojavax.bio.Bioentry and a Sequence.
RichSequenceIterator Essentially the same as SequenceIterator.

Classes in org.biojavax.bio.seq used by org.biojavax.bio.db.biosql

Class and Description
DummyRichSequenceHandler
RichLocation Describes locations, and adds the concepts of circularity, fuzziness, annotations, and cross-references to other databases.
RichLocation.Strand This class represents a strand on which a location may lie.
RichSequence A rich sequence is a combination of a org.biojavax.bio.Bioentry and a Sequence.
RichSequenceHandler An interface for classes that know how to handle subsequence operations.

Classes in org.biojavax.bio.seq used by org.biojavax.bio.db.ncbi

Class and Description
RichSequence A rich sequence is a combination of a org.biojavax.bio.Bioentry and a Sequence.

Classes in org.biojavax.bio.seq used by org.biojavax.bio.seq

Class and Description
CompoundRichLocation An implementation of RichLocation which covers multiple locations, but on the same strand of the same (optionally circular) sequence.
Position Holds info about base positions.
PositionResolver Resolves a position that is fuzzy or covers a range of bases by converting it to a single base.
RichFeature Represents a feature that can be given name and rank and be moved from one sequence to another.
RichFeatureRelationship Represents the relation between two features.
RichFeatureRelationshipHolder Holds feature relationships.
RichLocation Describes locations, and adds the concepts of circularity, fuzziness, annotations, and cross-references to other databases.
RichLocation.Strand This class represents a strand on which a location may lie.
RichSequence A rich sequence is a combination of a org.biojavax.bio.Bioentry and a Sequence.
RichSequenceHandler An interface for classes that know how to handle subsequence operations.
RichSequenceIterator Essentially the same as SequenceIterator.
SimpleRichLocation A simple implementation of RichLocation.
ThinRichSequence A simple implementation of RichSequence.

Classes in org.biojavax.bio.seq used by org.biojavax.bio.seq.io

Class and Description
RichFeature Represents a feature that can be given name and rank and be moved from one sequence to another.
RichLocation Describes locations, and adds the concepts of circularity, fuzziness, annotations, and cross-references to other databases.
RichSequence A rich sequence is a combination of a org.biojavax.bio.Bioentry and a Sequence.
RichSequence.Terms Stores a number of useful terms used across many sequence formats for consistency's sake.
RichSequenceIterator Essentially the same as SequenceIterator.